Yellow, Gold, Silver, and Crystal were all properly colored. Though Yellow did have a fair amount of Yellow pigments in most of the sprites, they were all still individually colored.

HG/SS got redesigns because the pixel art for the sprites weren't as clear as the third Gen sprites and didn't hold detail well. Between Gens 1 and 2 the Kanto Gym Leaders received clothing make overs, so between 3 and 4's remakes of them they'd do the same cause that was a relation they had in the originals.

There really just wasn't any reason to redesign the Hoenn leaders past updating them to larger sprites.